documentation/merge_samples.md

In anttonalberdi/hilldiv: Integral Analysis of Diversity Based on Hill Numbers

merge_samples()

Last update: hilldiv 1.5.3

Some diversity analyses, such as comparisons between species that contain multiple samples in the OTU or ASV table, require per-species count information. This function enables merging the count data of samples belonging to the same group, as specified in a hierarchy table.,

Arguments

| Arguments | Description | | ------------- | ------------- | | countable | A count table (matrix/data.frame) indicating the absolute or relative OTU/ASV abundances of multiple samples. Columns must refer to samples and rows to OTUs/ASVs. | | hierarchy | A two-column matrix indicating the relation between samples (first column) and groups (second column). | | relative | Whether to output relative values or not. Default=TRUE. | | incidence | Whether to transform abundance into incidence data when merging. Default=FALSE. |

Examples

data(bat.diet.otutable)
data(bat.diet.hierarchy)
merge_samples(countable=bat.diet.otutable,hierarchy=bat.diet.hierarchy)
merge_samples(bat.diet.otutable,bat.diet.hierarchy)
merge_samples(countable=bat.diet.otutable,hierarchy=bat.diet.hierarchy, incidence=TRUE)

anttonalberdi/hilldiv documentation built on Feb. 14, 2021, 5:08 p.m.